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CHECK report for QSutils on malbec2

This page was generated on 2019-10-16 12:16:40 -0400 (Wed, 16 Oct 2019).

Package 1291/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QSutils 1.2.0
Mercedes Guerrero-Murillo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/QSutils
Branch: RELEASE_3_9
Last Commit: b22533c
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QSutils
Version: 1.2.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QSutils_1.2.0.tar.gz
StartedAt: 2019-10-16 04:13:01 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:14:21 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 80.4 seconds
RetCode: 0
Status:  OK 
CheckDir: QSutils.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:QSutils.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings QSutils_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/QSutils.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QSutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QSutils’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘QSutils’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

QSutils.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL QSutils
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘QSutils’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (QSutils)

Tests output


Example timings

QSutils.Rcheck/QSutils-Ex.timings

nameusersystemelapsed
Collapse0.1470.0070.221
ConsSeq0.0280.0030.037
CorrectGapsAndNs0.0050.0040.008
DBrule0.0590.0130.080
DNA.dist0.0100.0000.011
DSFT0.0090.0000.009
Diverge0.0030.0000.003
DottedAlignment0.0120.0000.013
FAD0.0090.0000.009
FreqMat0.0170.0070.024
GenerateVars0.0050.0000.005
GenotypeStandards_A-H.fas0.0090.0000.008
GetInfProfile0.0280.0000.028
GetQSData0.5490.0120.561
GetRandomSeq000
GiniSimpson0.0000.0010.001
HCq0.0060.0020.006
Hill0.0060.0000.005
IntersectStrandHpls0.1140.0000.125
MutationFreq0.5930.0200.613
MutsTbl0.0200.0040.024
NucleotideDiversity0.0090.0000.009
PolyDist0.0360.0000.036
Rao0.0180.0000.018
ReadAmplSeqs0.0380.0000.038
Renyi0.0050.0000.006
ReportVariants0.0240.0000.024
SegSites0.0140.0000.013
Shannon0.0010.0000.001
SortByMutations0.6330.0000.632
SummaryMuts0.0240.0000.025
TotalMutations0.0220.0000.023
Toy.GapsAndNs.fna0.0650.0000.064
ToyData_10_50_1000.fna0.0360.0000.037
ToyData_FWReads.fna0.0990.0000.098
ToyData_RVReads.fna0.0940.0000.094
UniqueMutations0.0140.0000.015
Unknown-Genotype.fna0.0130.0000.012
fn.ab0.0040.0000.005
geom.series0.0030.0000.004